Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

Abhishek Singharoy; Ivan Teo; Ryan McGreevy; John E. Stone; Jianhua Zhao; Klaus Schulten

doi:10.7554/eLife.16105

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, Klaus Schulten

Research output: Contribution to journal › Article › peer-review

115 Scopus citations

Abstract

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of b-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Original language	English (US)
Article number	e16105
Journal	eLife
Volume	5
Issue number	JULY
DOIs	https://doi.org/10.7554/eLife.16105
State	Published - Jul 7 2016
Externally published	Yes

ASJC Scopus subject areas

General Neuroscience
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology

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title = "Molecular dynamics-based refinement and validation for sub-5 {\AA} cryo-electron microscopy maps",

abstract = "Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 {\AA} cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 {\AA} demonstrated with the accurate modeling of b-galactosidase and TRPV1 proteins at 3.2 {\AA} and 3.4 {\AA} resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.",

author = "Abhishek Singharoy and Ivan Teo and Ryan McGreevy and Stone, {John E.} and Jianhua Zhao and Klaus Schulten",

note = "Funding Information: This work is supported by grants NIH 9P41GM104601, NIH 5R01GM098243-02, and NIH U54GM087519 from the National Institutes of Health. The authors gratefully acknowledge computer time provided by the NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE) MCA93S028, Sriram Subramanian for extremely insightful discussions on the high-resolution cryo- EM methods in general, and the β-galactosidase study in particular, and Benjamin Barad from the Fraser group at UCSF for guidance on the use of the EMRinger program. The authors also acknowl- edge the Beckman Postdoctoral Fellowship program for supporting A Singharoy. Publisher Copyright: {\textcopyright} Singharoy et al.",

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AU - Zhao, Jianhua

AU - Schulten, Klaus

N1 - Funding Information: This work is supported by grants NIH 9P41GM104601, NIH 5R01GM098243-02, and NIH U54GM087519 from the National Institutes of Health. The authors gratefully acknowledge computer time provided by the NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE) MCA93S028, Sriram Subramanian for extremely insightful discussions on the high-resolution cryo- EM methods in general, and the β-galactosidase study in particular, and Benjamin Barad from the Fraser group at UCSF for guidance on the use of the EMRinger program. The authors also acknowl- edge the Beckman Postdoctoral Fellowship program for supporting A Singharoy. Publisher Copyright: © Singharoy et al.

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Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

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